Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,225,037 |
(T)6→5 |
coding (148/1434 nt) |
ygjI → |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,225,032 | 0 | T | . | 92.8%
| 256.2
/ 14.8
| 69 | coding (143/1434 nt) | ygjI | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/4); new base . (33/31); total (34/35) |
| Fisher's exact test for biased strand distribution p-value = 3.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
AACGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAAGC > W3110S.gb/3224968‑3225098
|
aacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttttat < 1:2649206/71‑3 (MQ=255)
aacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTtttta < 1:2188416/71‑1 (MQ=255)
aacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTtttta < 1:2100348/71‑1 (MQ=255)
aacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTtttta < 1:3712322/71‑1 (MQ=255)
aacGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTtttta < 1:1883360/71‑1 (MQ=255)
aTCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTtttattttat > 1:943300/1‑70 (MQ=255)
aTCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTttattttatt > 1:4023655/1‑71 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:2645528/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:1141635/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:2294658/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:796618/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:352474/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:1567558/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc < 1:355606/71‑1 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTcc > 1:2527773/1‑70 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTcc > 1:521561/1‑70 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTcc > 1:845551/1‑70 (MQ=255)
aataataatATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTcc > 1:1103947/1‑70 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAttttt < 1:1380650/56‑1 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtct > 1:2102107/1‑71 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtct > 1:1903905/1‑71 (MQ=255)
ataataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2287495/1‑70 (MQ=255)
taataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttttat < 1:3194550/57‑3 (MQ=255)
taataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctg < 1:3829691/71‑1 (MQ=255)
taataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctg < 1:2488605/71‑1 (MQ=255)
taataTTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc < 1:340472/69‑1 (MQ=255)
atatTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtc > 1:2243915/1‑71 (MQ=255)
atatTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtc > 1:2426104/1‑71 (MQ=255)
tatTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCt < 1:2111828/64‑1 (MQ=255)
atagAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:2689506/4‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:415131/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:1107040/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:2182347/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:2373922/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:1283659/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:2162188/1‑62 (MQ=255)
atTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTccc > 1:1614825/1‑62 (MQ=255)
ttGAGTTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:961815/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:1712501/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:3169257/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:3078398/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:3071419/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:53503/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:785914/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:3447338/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGAtttt < 1:1183426/49‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtctg < 1:295680/70‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtctg < 1:3295398/70‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtctg < 1:1360202/70‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtctg < 1:2609534/70‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgtctg < 1:511835/70‑1 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2504744/1‑64 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2942713/1‑64 (MQ=255)
ttGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtc > 1:2237540/1‑64 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatca < 1:2152047/65‑1 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatca < 1:1749959/65‑1 (MQ=255)
gACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGatca < 1:3650857/65‑1 (MQ=255)
aCTGGCCTCGGCACCGATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:4086842/57‑1 (MQ=255)
aCCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGt > 1:2623230/1‑71 (MQ=255)
gaggTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:621677/4‑71 (MQ=255)
gATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:2531614/1‑71 (MQ=255)
gATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:364518/1‑71 (MQ=255)
gATGTTTTTCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:3203821/1‑71 (MQ=255)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:3005117/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:998228/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:984215/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:2602443/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:925257/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:1321196/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:1497663/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:3374585/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTtctgt < 1:2095029/38‑1 (MQ=38)
tttttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaataaa < 1:2601916/71‑1 (MQ=255)
tttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:3066263/1‑65 (MQ=255)
tttCCTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTtaaa > 1:3738270/1‑65 (MQ=255)
ccTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACt > 1:229275/1‑70 (MQ=255)
ccTCGCGACGA‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACt > 1:3392742/1‑70 (MQ=255)
cgcgACTA‑TTTTTATTTTATTCCCTTCTGTCTTatca < 1:2994759/37‑1 (MQ=21)
gacga‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAAGc > 1:51122/1‑71 (MQ=255)
gacga‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAAGc > 1:2910355/1‑71 (MQ=255)
gacga‑TTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAAGc > 1:3566270/1‑71 (MQ=255)
|
AACGTTATCAATAATAATATTGAGCTTGGACTGGCCTCGGCACCGATGTTTTTCCTCGCGACGATTTTTTATTTTATTCCCTTCTGTCTGATCATCGCAGAATTTGTTTCGTTAAATAAAAACTCAGAAGC > W3110S.gb/3224968‑3225098
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
